AUTHOR=Suiter Nathan , Volkán-Kacsó Sándor 

TITLE=Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=10

YEAR=2023

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1184249

DOI=10.3389/fmolb.2023.1184249

ISSN=2296-889X

ABSTRACT=<p>A model-based method is used to extract a short-lived state in the rotation kinetics of the F<sub>1</sub>-ATPase of a bacterial species, Paracoccus denitrificans (PdF1). Imaged as a single molecule, PdF1 takes large 120<sup><italic>ø</italic></sup> steps during it rotation. The apparent lack of further substeps in the trajectories not only renders the rotation of PdF1 unlike that of other F-ATPases, but also hinders the establishment of its mechano-chemical kinetic scheme. We addressed these challenges using the angular velocity extracted from the single-molecule trajectories and compare it with its theoretically calculated counterpart. The theory-experiment comparison indicate the presence of a 20<italic>μ</italic>s lifetime state, 40<sup><italic>o</italic></sup> after ATP binding. We identify a kinetic cycle in which this state is a three-nucleotide occupancy state prior to ADP release from another site. A similar state was also reported in our earlier study of the Thermophilic <italic>bacillus</italic> F<sub>1</sub>-ATPase (lifetime <inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>∼</mml:mo><mml:mn>10</mml:mn><mml:mi>μ</mml:mi></mml:math></inline-formula>s), suggesting thereby a common mechanism for removing a nucleotide release bottleneck in the rotary mechanism.</p>